Patched 183,184,179,178 for 2.2.1

[GallVp]

PR checklist

• Patched HIC section in the report should say that a HTTPS server is needed! #183, plotsr failed on memverge with the error "Path value cannot be null" #184, Parameter validation failed for --hic #179, Update the flowchart #178 for 2.2.1
• If you've fixed a bug or added code that should be tested, add tests!
• If you've added a new tool - have you followed the pipeline conventions in the contribution docs
• Make sure your code lints (nf-core pipelines lint).
• Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).
• Check for unexpected warnings in debug mode (nextflow run . -profile debug,test,docker --outdir <OUTDIR>).
• Usage Documentation in docs/usage.md is updated.
• Output Documentation in docs/output.md is updated.
• CHANGELOG.md is updated.
• README.md is updated (including new tool citations and authors/contributors).

[github-actions]

This PR is against the main branch ❌

• Do not close this PR
• Click Edit and change the base to dev
• This CI test will remain failed until you push a new commit

---

Hi @GallVp,

It looks like this pull-request is has been made against the Plant-Food-Research-Open/assemblyqc main branch.
The main branch on nf-core repositories should always contain code from the latest release.
Because of this, PRs to main are only allowed if they come from the Plant-Food-Research-Open/assemblyqc dev branch.

You do not need to close this PR, you can change the target branch to dev by clicking the "Edit" button at the top of this page.
Note that even after this, the test will continue to show as failing until you push a new commit.

Thanks again for your contribution!

[github-actions]

nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 0439cbf

+| ✅ 166 tests passed       |+
#| ❔  33 tests were ignored |#
!| ❗   1 tests had warnings |!

❗ Test warnings:

• schema_lint - Schema $id should be https://raw.githubusercontent.com/plant-food-research-open/assemblyqc/master/nextflow_schema.json
  Found https://raw.githubusercontent.com/plant-food-research-open/assemblyqc/main/nextflow_schema.json

❔ Tests ignored:

• files_exist - File is ignored: conf/igenomes.config
• files_exist - File is ignored: conf/igenomes_ignored.config
• files_exist - File is ignored: assets/multiqc_config.yml
• files_exist - File is ignored: CODE_OF_CONDUCT.md
• files_exist - File is ignored: assets/nf-core-assemblyqc_logo_light.png
• files_exist - File is ignored: docs/images/nf-core-assemblyqc_logo_light.png
• files_exist - File is ignored: docs/images/nf-core-assemblyqc_logo_dark.png
• files_exist - File is ignored: .github/ISSUE_TEMPLATE/config.yml
• files_exist - File is ignored: .github/workflows/awstest.yml
• files_exist - File is ignored: .github/workflows/awsfulltest.yml
• nextflow_config - Config variable ignored: manifest.name
• nextflow_config - Config variable ignored: manifest.homePage
• nextflow_config - Config variable ignored: validation.help.beforeText
• nextflow_config - Config variable ignored: validation.help.afterText
• nextflow_config - Config variable ignored: validation.summary.beforeText
• nextflow_config - Config variable ignored: validation.summary.afterText
• files_unchanged - File does not exist: CODE_OF_CONDUCT.md
• files_unchanged - File ignored due to lint config: LICENSE or LICENSE.md or LICENCE or LICENCE.md
• files_unchanged - File ignored due to lint config: .github/CONTRIBUTING.md
• files_unchanged - File does not exist: .github/ISSUE_TEMPLATE/config.yml
• files_unchanged - File ignored due to lint config: .github/PULL_REQUEST_TEMPLATE.md
• files_unchanged - File ignored due to lint config: .github/workflows/branch.yml
• files_unchanged - File ignored due to lint config: .github/workflows/linting.yml
• files_unchanged - File does not exist: assets/nf-core-assemblyqc_logo_light.png
• files_unchanged - File does not exist: docs/images/nf-core-assemblyqc_logo_light.png
• files_unchanged - File does not exist: docs/images/nf-core-assemblyqc_logo_dark.png
• files_unchanged - File ignored due to lint config: docs/README.md
• files_unchanged - File ignored due to lint config: .gitignore or .prettierignore
• actions_ci - actions_ci
• actions_awstest - 'awstest.yml' workflow not found: /home/runner/work/assemblyqc/assemblyqc/.github/workflows/awstest.yml
• template_strings - template_strings
• multiqc_config - multiqc_config
• included_configs - included_configs

✅ Tests passed:

• files_exist - File found: .gitattributes
• files_exist - File found: .gitignore
• files_exist - File found: .nf-core.yml
• files_exist - File found: .editorconfig
• files_exist - File found: .prettierignore
• files_exist - File found: .prettierrc.yml
• files_exist - File found: CHANGELOG.md
• files_exist - File found: CITATIONS.md
• files_exist - File found: LICENSE or LICENSE.md or LICENCE or LICENCE.md
• files_exist - File found: nextflow_schema.json
• files_exist - File found: nextflow.config
• files_exist - File found: README.md
• files_exist - File found: .github/.dockstore.yml
• files_exist - File found: .github/CONTRIBUTING.md
• files_exist - File found: .github/ISSUE_TEMPLATE/bug_report.yml
• files_exist - File found: .github/ISSUE_TEMPLATE/feature_request.yml
• files_exist - File found: .github/PULL_REQUEST_TEMPLATE.md
• files_exist - File found: .github/workflows/branch.yml
• files_exist - File found: .github/workflows/ci.yml
• files_exist - File found: .github/workflows/linting_comment.yml
• files_exist - File found: .github/workflows/linting.yml
• files_exist - File found: assets/email_template.html
• files_exist - File found: assets/email_template.txt
• files_exist - File found: assets/sendmail_template.txt
• files_exist - File found: conf/modules.config
• files_exist - File found: conf/test.config
• files_exist - File found: conf/test_full.config
• files_exist - File found: docs/output.md
• files_exist - File found: docs/README.md
• files_exist - File found: docs/README.md
• files_exist - File found: docs/usage.md
• files_exist - File found: main.nf
• files_exist - File found: conf/base.config
• files_exist - File found: modules.json
• files_exist - File not found check: .github/ISSUE_TEMPLATE/bug_report.md
• files_exist - File not found check: .github/ISSUE_TEMPLATE/feature_request.md
• files_exist - File not found check: .github/workflows/push_dockerhub.yml
• files_exist - File not found check: .markdownlint.yml
• files_exist - File not found check: .nf-core.yaml
• files_exist - File not found check: .yamllint.yml
• files_exist - File not found check: bin/markdown_to_html.r
• files_exist - File not found check: conf/aws.config
• files_exist - File not found check: docs/images/nf-core-assemblyqc_logo.png
• files_exist - File not found check: lib/Checks.groovy
• files_exist - File not found check: lib/Completion.groovy
• files_exist - File not found check: lib/NfcoreTemplate.groovy
• files_exist - File not found check: lib/Utils.groovy
• files_exist - File not found check: lib/Workflow.groovy
• files_exist - File not found check: lib/WorkflowMain.groovy
• files_exist - File not found check: lib/WorkflowAssemblyqc.groovy
• files_exist - File not found check: parameters.settings.json
• files_exist - File not found check: pipeline_template.yml
• files_exist - File not found check: Singularity
• files_exist - File not found check: lib/nfcore_external_java_deps.jar
• files_exist - File not found check: .travis.yml
• nextflow_config - Found nf-schema plugin
• nextflow_config - Config variable found: manifest.nextflowVersion
• nextflow_config - Config variable found: manifest.description
• nextflow_config - Config variable found: manifest.version
• nextflow_config - Config variable found: timeline.enabled
• nextflow_config - Config variable found: trace.enabled
• nextflow_config - Config variable found: report.enabled
• nextflow_config - Config variable found: dag.enabled
• nextflow_config - Config variable found: process.cpus
• nextflow_config - Config variable found: process.memory
• nextflow_config - Config variable found: process.time
• nextflow_config - Config variable found: params.outdir
• nextflow_config - Config variable found: params.input
• nextflow_config - Config variable found: validation.help.enabled
• nextflow_config - Config variable found: manifest.mainScript
• nextflow_config - Config variable found: timeline.file
• nextflow_config - Config variable found: trace.file
• nextflow_config - Config variable found: report.file
• nextflow_config - Config variable found: dag.file
• nextflow_config - Config variable found: validation.help.command
• nextflow_config - Config variable (correctly) not found: params.nf_required_version
• nextflow_config - Config variable (correctly) not found: params.container
• nextflow_config - Config variable (correctly) not found: params.singleEnd
• nextflow_config - Config variable (correctly) not found: params.igenomesIgnore
• nextflow_config - Config variable (correctly) not found: params.name
• nextflow_config - Config variable (correctly) not found: params.enable_conda
• nextflow_config - Config variable (correctly) not found: params.max_cpus
• nextflow_config - Config variable (correctly) not found: params.max_memory
• nextflow_config - Config variable (correctly) not found: params.max_time
• nextflow_config - Config variable (correctly) not found: params.validationFailUnrecognisedParams
• nextflow_config - Config variable (correctly) not found: params.validationLenientMode
• nextflow_config - Config variable (correctly) not found: params.validationSchemaIgnoreParams
• nextflow_config - Config variable (correctly) not found: params.validationShowHiddenParams
• nextflow_config - Config timeline.enabled had correct value: true
• nextflow_config - Config report.enabled had correct value: true
• nextflow_config - Config trace.enabled had correct value: true
• nextflow_config - Config dag.enabled had correct value: true
• nextflow_config - Config dag.file ended with .html
• nextflow_config - Config variable manifest.nextflowVersion started with >= or !>=
• nextflow_config - Config manifest.version does not contain dev for release: 2.2.1
• nextflow_config - Config params.custom_config_version is set to master
• nextflow_config - Config params.custom_config_base is set to https://raw.githubusercontent.com/nf-core/configs/master
• nextflow_config - Lines for loading custom profiles found
• nextflow_config - nextflow.config contains configuration profile test
• nextflow_config - Config default value correct: params.check_sequence_duplicates= true
• nextflow_config - Config default value correct: params.assemblathon_stats_n_limit= 100
• nextflow_config - Config default value correct: params.gfastats_skip= true
• nextflow_config - Config default value correct: params.ncbi_fcs_adaptor_skip= true
• nextflow_config - Config default value correct: params.ncbi_fcs_gx_skip= true
• nextflow_config - Config default value correct: params.contamination_stops_pipeline= true
• nextflow_config - Config default value correct: params.tidk_skip= true
• nextflow_config - Config default value correct: params.tidk_filter_size_bp= 1000000
• nextflow_config - Config default value correct: params.busco_skip= true
• nextflow_config - Config default value correct: params.lai_skip= true
• nextflow_config - Config default value correct: params.kraken2_skip= true
• nextflow_config - Config default value correct: params.hic_fastp_ext_args= --qualified_quality_phred 20 --length_required 50
• nextflow_config - Config default value correct: params.hic_samtools_ext_args= -F 3852
• nextflow_config - Config default value correct: params.merqury_skip= true
• nextflow_config - Config default value correct: params.merqury_kmer_length= 21
• nextflow_config - Config default value correct: params.synteny_skip= true
• nextflow_config - Config default value correct: params.synteny_mummer_skip= true
• nextflow_config - Config default value correct: params.synteny_plotsr_skip= true
• nextflow_config - Config default value correct: params.synteny_between_input_assemblies= true
• nextflow_config - Config default value correct: params.synteny_mummer_plot_type= both
• nextflow_config - Config default value correct: params.synteny_mummer_max_gap= 1000000
• nextflow_config - Config default value correct: params.synteny_mummer_min_bundle_size= 1000000
• nextflow_config - Config default value correct: params.synteny_color_by_contig= true
• nextflow_config - Config default value correct: params.synteny_plotsr_seq_label= Chr
• nextflow_config - Config default value correct: params.orthofinder_skip= true
• nextflow_config - Config default value correct: params.custom_config_version= master
• nextflow_config - Config default value correct: params.custom_config_base= https://raw.githubusercontent.com/nf-core/configs/master
• nextflow_config - Config default value correct: params.publish_dir_mode= copy
• files_unchanged - .gitattributes matches the template
• files_unchanged - .prettierrc.yml matches the template
• files_unchanged - .github/.dockstore.yml matches the template
• files_unchanged - .github/ISSUE_TEMPLATE/bug_report.yml matches the template
• files_unchanged - .github/ISSUE_TEMPLATE/feature_request.yml matches the template
• files_unchanged - .github/workflows/linting_comment.yml matches the template
• files_unchanged - assets/email_template.html matches the template
• files_unchanged - assets/email_template.txt matches the template
• files_unchanged - assets/sendmail_template.txt matches the template
• readme - README Nextflow minimum version badge matched config. Badge: 24.04.2, Config: 24.04.2
• readme - README Zenodo placeholder was replaced with DOI.
• pipeline_todos - No TODO strings found
• plugin_includes - No wrong validation plugin imports have been found
• pipeline_name_conventions - Name adheres to nf-core convention
• schema_lint - Schema lint passed
• schema_lint - Input mimetype lint passed: 'text/csv'
• schema_params - Schema matched params returned from nextflow config
• system_exit - No System.exit calls found
• actions_schema_validation - Workflow validation passed: linting.yml
• actions_schema_validation - Workflow validation passed: branch.yml
• actions_schema_validation - Workflow validation passed: download_pipeline.yml
• actions_schema_validation - Workflow validation passed: ci.yml
• actions_schema_validation - Workflow validation passed: clean-up.yml
• actions_schema_validation - Workflow validation passed: linting_comment.yml
• merge_markers - No merge markers found in pipeline files
• modules_json - Only installed modules found in modules.json
• modules_structure - modules directory structure is correct 'modules/nf-core/TOOL/SUBTOOL'
• base_config - conf/base.config found and not ignored.
• base_config - NCBI_FCS_GX_SCREEN_SAMPLES found in conf/base.config and Nextflow scripts.
• base_config - KRAKEN2 found in conf/base.config and Nextflow scripts.
• base_config - BWA_MEM found in conf/base.config and Nextflow scripts.
• base_config - SAMBLASTER found in conf/base.config and Nextflow scripts.
• base_config - DNADIFF found in conf/base.config and Nextflow scripts.
• base_config - MERQURY_HAPMERS found in conf/base.config and Nextflow scripts.
• base_config - CREATEREPORT found in conf/base.config and Nextflow scripts.
• modules_config - conf/modules.config found and not ignored.
• nfcore_yml - Repository type in .nf-core.yml is valid: pipeline
• nfcore_yml - nf-core version in .nf-core.yml is set to the latest version: 3.0.2
• version_consistency - Version tags are numeric and consistent between container, release tag and config.

Run details

• nf-core/tools version 3.0.2
• Run at 2024-12-11 02:44:17